Bottom Line:
Wildlife may facilitate the spread of antibiotic resistance (AR) between human-dominated habitats and the surrounding environment.An analysis of the flanking sequences indicates that most of these genes are present in Enterobacteriaceae and various Gram-positive bacteria.These undescribed genes include one most similar to an uncharacterized gene in Verrucomicrobium and another to a putative DNA repair protein in Lactobacillus.

Affiliation: Department of Earth System Science, University of California Irvine, CA, USA.

ABSTRACTWildlife may facilitate the spread of antibiotic resistance (AR) between human-dominated habitats and the surrounding environment. Here, we use functional metagenomics to survey the diversity and genomic context of AR genes in gulls. Using this approach, we found a variety of AR genes not previously detected in gulls and wildlife, including class A and C β-lactamases as well as six tetracycline resistance gene types. An analysis of the flanking sequences indicates that most of these genes are present in Enterobacteriaceae and various Gram-positive bacteria. In addition to finding known gene types, we detected 31 previously undescribed AR genes. These undescribed genes include one most similar to an uncharacterized gene in Verrucomicrobium and another to a putative DNA repair protein in Lactobacillus. Overall, the study more than doubled the number of clinically relevant AR gene types known to be carried by gulls or by wildlife in general. Together with the propensity of gulls to visit human-dominated habitats, this high diversity of AR gene types suggests that gulls could facilitate the spread of AR.

Figure 3: Phylogenetic tree of the bl1_ec type class C β-lactamase gene from metagenomic clones and sequenced representative strains from ARDB. The sequenced clones are from samples from gulls or soil, whereas we did not detect any bl1_ec type clones in samples from wastewater. Metagenomic clones were isolated on ampicillin, amoxicillin, or penicillin as listed for each entry. The phylogenetic tree is a majority rule consensus tree based on protein similarity using neighbor-joining. Bootstrap values (total 100) are calculated with neighbor-joining and maximum likelihood methods. Edwardsiella tarda sp. EIB202 is the outgroup.

Mentions:
In addition to detecting multiple classes of AR genes, we found several DNA polymorphisms in the bl1_ec type. To further explore this result, we aligned the sequences matching this ARDB type and built a phylogenetic tree (Figure 3). All gull bl1_ec sequences grouped with E. coli 1.1.43 with high bootstrap support. In contrast, sequences retrieved from the soil samples formed three separate clades, with only one soil clone clustering with the gull variants. Instead, the one clade of soil AR sequences were 100% similar to E. coli H120, whereas the other genes branched away from known E. coli genes. Overall, this indicates that the bl1_ec diversity is related to its environmental origin. We also analyzed the sequence variation among clones from the RAHN-2 β-lactamase genes but only observed one variant.

Figure 3: Phylogenetic tree of the bl1_ec type class C β-lactamase gene from metagenomic clones and sequenced representative strains from ARDB. The sequenced clones are from samples from gulls or soil, whereas we did not detect any bl1_ec type clones in samples from wastewater. Metagenomic clones were isolated on ampicillin, amoxicillin, or penicillin as listed for each entry. The phylogenetic tree is a majority rule consensus tree based on protein similarity using neighbor-joining. Bootstrap values (total 100) are calculated with neighbor-joining and maximum likelihood methods. Edwardsiella tarda sp. EIB202 is the outgroup.

Mentions:
In addition to detecting multiple classes of AR genes, we found several DNA polymorphisms in the bl1_ec type. To further explore this result, we aligned the sequences matching this ARDB type and built a phylogenetic tree (Figure 3). All gull bl1_ec sequences grouped with E. coli 1.1.43 with high bootstrap support. In contrast, sequences retrieved from the soil samples formed three separate clades, with only one soil clone clustering with the gull variants. Instead, the one clade of soil AR sequences were 100% similar to E. coli H120, whereas the other genes branched away from known E. coli genes. Overall, this indicates that the bl1_ec diversity is related to its environmental origin. We also analyzed the sequence variation among clones from the RAHN-2 β-lactamase genes but only observed one variant.

Bottom Line:
Wildlife may facilitate the spread of antibiotic resistance (AR) between human-dominated habitats and the surrounding environment.An analysis of the flanking sequences indicates that most of these genes are present in Enterobacteriaceae and various Gram-positive bacteria.These undescribed genes include one most similar to an uncharacterized gene in Verrucomicrobium and another to a putative DNA repair protein in Lactobacillus.

Affiliation:
Department of Earth System Science, University of California Irvine, CA, USA.

ABSTRACTWildlife may facilitate the spread of antibiotic resistance (AR) between human-dominated habitats and the surrounding environment. Here, we use functional metagenomics to survey the diversity and genomic context of AR genes in gulls. Using this approach, we found a variety of AR genes not previously detected in gulls and wildlife, including class A and C β-lactamases as well as six tetracycline resistance gene types. An analysis of the flanking sequences indicates that most of these genes are present in Enterobacteriaceae and various Gram-positive bacteria. In addition to finding known gene types, we detected 31 previously undescribed AR genes. These undescribed genes include one most similar to an uncharacterized gene in Verrucomicrobium and another to a putative DNA repair protein in Lactobacillus. Overall, the study more than doubled the number of clinically relevant AR gene types known to be carried by gulls or by wildlife in general. Together with the propensity of gulls to visit human-dominated habitats, this high diversity of AR gene types suggests that gulls could facilitate the spread of AR.